2 Answers
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WinMerge is an Open Source differencing and merging tool for Windows. WinMerge can compare both folders and files, presenting differences in a visual text format that is easy to understand and handle.

If you want something more powerful, try BeyondCompare. It's not free but it has a free 30 day trial if you want to test it out.

Beyond Compare allows you to quickly and easily compare your files and folders. By using simple, powerful commands you can focus on the differences you're interested in and ignore those you're not. You can then merge the changes, synchronize your files, and generate reports for your records.

Do these programs write to the data while comparing without my permission (i.e merge them) ?? Say beyondcompare for instance..
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ramyyDec 21 '12 at 7:19

These programs don't change any data, they just analyze drive or folder contents, and display the results. Additionally Beyond Compare has a feature that will help you merge differences and changes, as stated on their website: By using simple, powerful commands you can focus on the differences you're interested in and ignore those you're not. You can then merge the changes, synchronize your files, and generate reports for your records.
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James YoungDec 21 '12 at 13:16

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Thanks, it's a great program and really helped..
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ramyyDec 21 '12 at 14:48

A diff utility will do what you want. It sounds like this is a one-time thing for you, so I think you'll be happy with the diff that's in the free version of my Hamilton C shell.

diff olddirectory newdirectory | more

The open source Cygwin diff would be another alternative but its output is a little different and might not be as useful, given what you're asking. (It's harder to get lists of files that have changed.) Try them both and see what you think.